Hello,
ok. Then i try this with java. I do the following:
private void loadMoleculefromFile(String filename){
try {
MDLV2000Reader reader = new MDLV2000Reader(new
FileReader(new File(filename)));
if(reader.read((ChemObject)new ChemFile()) != null){
ChemFile chemFile =
(ChemFile)reader.read((ChemObject)new ChemFile());
List<IAtomContainer> containersList =
ChemFileManipulator.getAllAtomContainers(chemFile);
int i=0;
for(IAtomContainer a : containersList){
System.out.println(a.toString() + "; "
+ i + "/" + containersList.size());
i++;
}
}
} catch (CDKException e) {
e.printStackTrace();
} catch (FileNotFoundException e) {
e.printStackTrace();
}
}
And call this function with:
loadMoleculefromFile("query.sdf");
And with:
loadMoleculefromFile("Compound_000000001_000025000.sdf");
With the last call i'll get the printouts.
The first call of the function works too but throws this exception:
java.lang.NullPointerException
at
org.openscience.cdk.io.MDLV2000Reader.readMolecule(MDLV2000Reader.java:395)
at
org.openscience.cdk.io.MDLV2000Reader.readChemFile(MDLV2000Reader.java:236)
at org.openscience.cdk.io.MDLV2000Reader.read(MDLV2000Reader.java:185)
at Main.loadMoleculefromFile(Main.java:146)
at Main.<init>(Main.java:45)
at Main.main(Main.java:41)
This in the 4-line or the 5-line (get the same error).
With the normal MDLReader it doesn't work for both files.
Have you an idea about this exception.
And how could i handle the similarity inside java?
Jochen
Am 22.11.2011 um 10:41 schrieb Egon Willighagen:
> On Tue, Nov 22, 2011 at 10:37 AM, Jochen Schreiber
> <[email protected]> wrote:
>> And i don't know how i could say to momsim.jar use the MDLV2000Reader.
>
> Neither do I; I don't know that jar. I suggest contacting the author.
>
> Egon
>
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Institutet för miljömedicin
> Karolinska Institutet (http://ki.se/imm)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
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